ArticleGenome research2009
Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 48 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
48 citing papers in PubMed.
- Chromosomal quality control in hPSCs: A practical guide to SNP array analysis with GenomeStudio.Frontiers in cell and developmental biology · 2025Article
- Potential role of miR-29b from mesenchymal stromal cell-derived extracellular vesicles in leukemic cell progression.PloS one · 2025Article
- Article
- Screening of in vitro-produced cattle embryos to assess incidence and characteristics of unbalanced chromosomal aberrations.JDS communications · 2023Article
- Inheritance of somatic mutations by animal offspring.Science advances · 2022Article
- FGFR1 is a potential therapeutic target in neuroblastoma.Cancer cell international · 2022Article
- Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma.Genome biology · 2022Article
- Article
- Fetal Megalencephaly with Cortical Dysplasia at 18 Gestational Weeks Related to Paternal UPD Mosaicism withGenes · 2021Article
- Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers.Planta · 2021Article
- A genome-wide analysis of copy number variation in Murciano-Granadina goats.Genetics, selection, evolution : GSE · 2020Article
- CNV Radar: an improved method for somatic copy number alteration characterization in oncology.BMC bioinformatics · 2020Article
- Accelerating development of high-risk neuroblastoma patient-derived xenograft models for preclinical testing and personalised therapy.British journal of cancer · 2020Article
- Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations.Cell systems · 2020Article
- Quantification of Multiple Tumor Clones Using Gene Array and Sequencing Data.The annals of applied statistics · 2017Article
- Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.Nature genetics · 2017Article
- Crizotinib Synergizes with Chemotherapy in Preclinical Models of Neuroblastoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2016Article
- BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor.Scientific reports · 2015Article
- Allele-specific copy-number discovery from whole-genome and whole-exome sequencing.Nucleic acids research · 2015Article
- Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?BMC genomics · 2014Article
Corrections and comments
- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
Microarrays are frequently used to profile genome-wide copy number (CN) aberrations. While generally robust for detecting CN variants in germline DNA, the methods used to derive CN from signal intensity values have been suboptimal when applied to cancer genomes. The complexity of genomic aberrations in cancer makes it more difficult to discriminate between signal and noise, and measuring CN as a discrete variable does not account for tumor heterogeneity. Furthermore, standard normalization approaches detect CN changes relative to the overall DNA content, which is often not diploid in cancer. We propose an algorithm that uses the degree of allelic imbalance as well as probe intensity, with a correction for aneuploidy, for a quantitative CN assessment and scoring of allelic ratios. This algorithm results in a more precise definition of CN and allelic aberration in the cancer genome, which is essential for translational efforts focused on using these tools for molecular diagnostics and for the discovery of therapeutic targets.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.